And when I tried running tophat alone like this: tophat -r 20 test_ref reads_1.fq reads_2.fq
I get this error: [2012-12-19 06:57:07] Beginning TopHat run (v2.0.7) ----------------------------------------------- [2012-12-19 06:57:07] Checking for Bowtie Bowtie version: 2.0.2.0 [2012-12-19 06:57:07] Checking for Samtools Samtools version: 0.1.18.0 [2012-12-19 06:57:07] Checking for Bowtie index files Error: Could not find Bowtie 2 index files (test_ref.*.bt On Wed, Dec 19, 2012 at 10:38 AM, Sachit Adhikari < sachit.techner...@gmail.com> wrote: > This is the error I am getting while running Tophat. What's causing this? > I have the default hg19 index files. > > Error in tophat: > > [Tue Dec 18 10:08:33 2012] Beginning TopHat run (v1.3.3) > ----------------------------------------------- > [Tue Dec 18 10:08:33 2012] Preparing output location ./tophat_out/ > [Tue Dec 18 10:08:33 2012] Checking for Bowtie index files > Error: Could not find Bowtie index files > /opt/galaxyprod/galaxy-dist/data/hg19/hg19,/data/bowtie2-2.0.2/hg19.* > > TopHat v1.3.3 > TopHat v1.3.3 > tophat -p 4 > /opt/galaxyprod/galaxy-dist/data/hg19/hg19,/data/bowtie2-2.0.2/hg19 > /opt/galaxyprod/galaxy-dist/database/files/000/dataset_45.dat > >
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